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Dear All, Thank you very much for valuable suggestions and educating me on the normal mode refinement. Actually, I am trying to refine a protein (cytosolic domain and trans-membrane domain). I found a solution through PHASER and density looks really good in both domain but as i proceeds with refinement density remain great in both domain till Rfree around 38%. Interestingly, with further refinement cycle, Rfree reduced to 30% but the density in the trans-membrane domain becomes very weak. That is why i am wondering whether it is possible to improve the density in the trans-membrane domain by using Normal mode refinement. Conservatively speaking, it could be possible that trans-membrane is highly flexible or disordered and after much cerebration, i am thinking to incorporate the normal mode refinement to monitor if there is any improvement in electron density trans-membrane domain. I would follow suggestions of Dr, Mande and Dr. Ethan. Also, would give a try to what Arpita has suggested. I further, warmly welcome any suggestion on refinement procedure to improve electron density in flexible or disordered trans-membrane domain. Appu On 20 October 2014 23:41, Arpita Goswami <[log in to unmask]> wrote: > Hello, > > You can also contact elNemo or NOMAD-Ref server developers about getting > covariance/correlation matrices from normal mode analysis outputs to know > the correctly coordinated mobile atoms. In this way you can compare with > biological data also. In Shekhar's said paper K. Suhre (one of the > developer of el-Nemo server) has done the same very correctly. > > best wishes, > Arpita > > On Tue, Oct 21, 2014 at 5:40 AM, Appu kumar <[log in to unmask]> wrote: > >> Dear CCP4 Users, >> I seek your valuable advice and suggestion in carrying out the normal >> mode structure refinement which manifest the dynamics of protein as linear >> combination of harmonic modes, used to describe the motion of protein >> structure in collective fashion. Studies suggest that it is highly useful >> in refining the protein structure which harbors a considerable magnitude of >> flexibility in atomic position owing to high thermal factors. >> Therefor I want to know is there any software/script available to execute >> the normal mode of refinement. Thanks a lot in advance for your imperative >> suggestions >> >> Appu >> > > > > -- > Arpita > > -- > Arpita Goswami > Senior Research Fellow > Structural Biology Laboratory > Centre for DNA Fingerprinting and Diagnostics (CDFD) > Tuljaguda (Opp MJ Market), > Nampally, Hyderabad 500 001 > INDIA > Phone: +91- 40- 24749401/404 > Mobile: 9390923667, 9502389184 > Email: [log in to unmask] >